Affliction
by JaceLover01
Summary: JACE/CLARY! Everything seems to be running smoothly with Clary's training to become a Shadowhunter...but soon things start to unravel when it is discovered that someone who they thought was dead and gone forever returns to destory once and for all.
1. Chapter 1

**So I've been thinking on this idea for about a month and I've finally started putting it into words. I've had the entire thing, chapter for chapter planned out in my head and I'm finally getting to it! So here we go. I hope you like the first chapter!**

**I'm starting a playlist to go along with my story and the song I thought fit for this chapter is **_**In Fate's Hands**_** by ****The Red Jumpsuit Apparatus****. You can find the playlist on my profile as it progresses and I'm also going to make a playlist on Playlist (dot) com. **

**[Disclaimer: I don't own it. The brilliant Cassandra Clare does.]**

**Chapter One**

Clary jerked awake when she heard her alarm clock go off on her bedside table noisily at eight in the morning, making her groan with pure annoyance. She wished she didn't have to do training today. She was still sore from the day before; she had bruises all over her body and her muscles ached in protest as she swung her legs over the side of her bed, pushing the snooze button on her clock to silence the damn thing. She ran a hand through the mass of tangled red curls that hung around her face.

"Clary! You have twenty minutes to meet me in the training room!" A voice called through the barrier of the wooden door. She heard footsteps right after the sentence, fading down the hallway. Usually Jace's voice made her heart skip a beat and a chill to race down her spine, but not today. Today she was too damn tired to feel like that.

Clary dropped her head into her hands and a groan escaped her lips. "You suck," she muttered under her breath before she pushed herself to her feet, looking at herself in the mirror, she saw her eyes were bloodshot and the expression on her face was one of irritation and weariness.

Standing up, Clary went over to her closet and grabbed a pair of sweatpants and a t-shirt that said "New Yorker" on it in black letters. She pulled her unruly mass of red hair up into a ponytail and examined herself in the mirror. She frowned at her reflection. She didn't know what Jace saw in her—just a short, pale girl with curly red hair and freckles. The one thing she hated about her appearance was her freckles. She thought that if she didn't have them, then she truly would be pretty. But they were an imperfection and she wanted them gone. She sighed softly. "This is as good as it's gonna get," she mumbled to herself before she walked into the bathroom attached to her bedroom. She washed her face and brushed her teeth before she walked out of her room, closing the door softly behind her.

A door opened down the hallway as she walked slowly to the torture room—as she called it—and Alec walked out and looked at her with a smile. "Going to training?"

Clary nodded. "Yeah, wouldn't want to disappoint King Jace," she said with a smile as she came to a stop several feet from Alec.

"Is he working you hard? Izzy said you were covered in bruises," Alec said and Clary caught the brief flash of concern in his eyes. She was glad they all cared about her. She just wished Jace would take training a bit easier. She didn't let him know about the bruises or else he would stop the training altogether and he'd stick her with Isabelle or Alec, and she needed him, the best Shadowhunter of their age group to teach her. In fact, she was convinced he was the best Shadowhunter in existence currently.

Clary sighed. "Isabelle was exaggerating. I'm fine. And don't let Jace hear you saying that okay? I don't want anything to interrupt training. The faster I can be out there with you guys the better. Maryse and my mom think it's best if I get trained properly first," she told him with a roll of her eyes.

Alec grimaced. "They just want to keep you safe. You're learning fast. You'll be coming along with us in no time," he said with a pat to her shoulder.

"Thanks, Alec," Clary said. She was about to ask him something when Jace walked around the corner.

"Clary," he said in that exaggeratedly impatient tone of his, blond hair messed up as if he hadn't even bothered to brush it after he woke up. "Your twenty minutes is up. Come on."

Clary heaved a sigh before she gave Alec a small smile. "See you later," she told him as she passed him to where Jace was standing, hands hanging loosely at his sides. He took hold of her hand when she got to him and he kissed her cheek. She liked the soft side of Jace. It was so unlike how he was with the others. She got special treatment and she took pride in that…well, special treatment until it was training time. Then the old Jace came out, but Clary didn't mind. She liked all sides of Jace's personality; cocky and sarcastic and sweet and tender. She didn't mind how he acted as long as he was near her.

"Trying to get out of training?" Jace asked with a smirk in her direction as

"As if I really could," Clary snorted with dry amusement. "You'd only just hunt me down and drag me there," she told him, but they both knew that wasn't true. He'd pick her up and take her there instead of dragging her.

Jace didn't reply and soon they were walking into the training room, sparring mats spread around, a punching bag nearby, some Styrofoam-like targets for knife throwing and such. It was a big room with a big window on the far wall, looking out over the street, buildings surrounding them.

"So what are we doing today?" Clary asked, fearing he would say hand-to-hand combat again. She thought that hand-to-hand combat could rot in hell for all she cared. She didn't want to be sore in the morning again.

Jace saw the look in her eyes and he smiled. "Just thirty minutes of combat training and then we're going to start you on knife throwing, alright?" he told her as he led her to the middle of the room where the mats were spread all around. He let go of her hand and walked five paces away before he turned around to face her once again.

Clary blew out a sigh, already able to feel her body screaming at her to not do it. "Alright," she agreed with a nod, taking up her defensive stance. Opposite her, Jace had an offensive stance and he slowly started moving forward.

In less than a second, he was grabbing her, trying to flip her onto her back. When she slammed her foot down on his instep, a barely audible breath hissed from his lips and she was able to get out of his hold on her. She turned and started throwing punches and kicks. He blocked every single one, anticipating each and every one of her moves.

Clary stumbled slightly over the mat and Jace took advantage of her momentary distraction to grab her and throw her down on the mat on her back. A gasp escaped Clary's lips as the breath was knocked out of her and Jace was straddling her waist in less than a second, pinning her hands on either side of her head.

Clary was breathing hard already but Jace didn't look out of breath in the least. His cocky grin was fixed back into place from where his serious "fighting expression" had been present.

"Pin," Jace said with a chuckle, leaning down to brush his lips against her neck. Clary sucked in a breath and it felt as if her heart faltered for a moment. How he could get that reaction out of her by such a simple action was beyond her.

Jace's grin widened as he noted her reaction and she narrowed her eyes, glaring up at him, but her heart wasn't in the angry look. The corners of her lips turned up in an almost smile. "Jace?" she said, making her voice soft as she looked up at him.

Jace looked back down at her, his beautiful eyes looking into hers. "Yes, Clary?" he asked, arching an eyebrow up in question.

His hands were gripping her arms a bit tighter than she would have liked but she didn't say anything. "I—"

But she didn't finish what she started to say because Isabelle walked in the training room in a pair of tight black jeans and a black halter top that fit her like it was painted on. She could pull off such looks but Clary knew that she would never be able to do that like Isabelle could.

"Jace," Isabelle said, her voice tight as she watched him hold Clary down on the mat. "Let her up—now."

When Isabelle had seen the light purple bruises on Clary's skin the day before she nearly went to Jace's room and gave him a taste of his own medicine, but Clary had begged her not to. She'd said that she just wasn't used to so much physical combat and she'd be fine in a few days. Isabelle didn't like it though.

Jace regarded Isabelle coolly. "Why?" he asked, a tone of challenge in his voice.

"Because you're hurting her! That's why," Isabelle said, walking forward, her black knee-high boots with a seven inch heel making a soft clicking noise as her shoes made contact with the floor.

Jace rolled his eyes. "Oh get real, Izzy. We're practicing," he said, letting go of Clary's hands and getting to his feet, helping her up too.

"Izzy, stop, please," Clary said, looking at the other girl, giving her a pointed look. She didn't want Jace freaking out over the bruises and he was sure to do that if Isabelle kept up talking.

"I wasn't hurting her," Jace said to Isabelle and something in his eyes made Clary unable to look away. She knew Valentine had hurt him while he had been growing up and it made him defensive to think that anyone was accusing him of hurting anyone he cared about, especially Clary.

Isabelle pursed her lips, looking from Jace to Clary, her hands on her hips while she tapped her boot against the floor.

Jace let out a frustrated sigh. "Clary," he said, voice strained. "Am I hurting you?"

"No," Clary said instantly, looking up at him. She didn't care about a few "battle scars" as she liked to call them. It just showed that she was trying hard and it gave her the motivation she needed to improve.

"See?" Jace said to Isabelle impatiently. "Now go away so we can continue."

Isabelle looked like she was about to protest but Clary gave her a pleading look that Jace couldn't see since she was standing in front of him with her back to him. The dark haired girl huffed. "Oh fine. I can see when I'm not wanted," she said before she turned on her heel and walked off, letting the door shut loudly behind her.

Clary let out a breath. Crisis adverted.

"Let's skip to target practice before Izzy comes back in and attacks me again," Jace told her as he led her over to where five knives were laying on a small table with a piece of fabric shielding the tabletop from the blades. "Now, watch and learn," he said before he flicked all five knives towards the Styrofoam target, almost faster than Clary's eyes could even comprehend. All five knives, Clary saw, were imbedded into the center, right on target.

Clary's eyes widened and she let out a breath before she looked up at him. "You're good."

Jace grinned and was about to say something but she gave him a look. "Don't be cocky," she told him.

"Suit yourself," Jace said as he went to retrieve the knives. He brought them back over to where Clary was and he handed them to her. "Give it a shot."

Clary took them and sighed, holding the five sharp objects in her hand. She picked one up with her right hand and aimed as well as she could before she let it fly through the air. It was stuck into the wall. Frowning, she threw all four others and they, too, were stuck into the walls.

"Good try," Jace said, but Clary knew he was just saying that. He went and plucked them from the Styrofoam before he returned. "Let me show you how to really—"

Alec burst into the room. "Jace, mom wants to see us in the library. She says it's urgent."

Before Jace could ask what it was about, Alec was already out the door again at a run. Jace put the knives down and grabbed Clary's small hand in his. "C'mon," he told her as he started walking swiftly out of the room, heading for the stairs.

Moments later, Clary was being dragged into the library where Maryse stood in the middle of the room. Alec and Isabelle were seated on the leather sofa.

"Jace, Clary, have a seat," Maryse told them, gesturing to the empty loveseat across from her children.

Clary felt nerves bubble in her stomach, wondering what on earth was so urgent. She saw a man dressed in the normal Shadowhunter black clothing, standing off to the side. He looked tough, she thought.

Jace tugged her over to the loveseat with him before he sat down with her. "What's this about?" he asked Maryse, casting a suspicious glance over at the Shadowhunter man who he obviously didn't know.

Maryse looked weary. "Someone who we thought to be dead…is very much alive and looking for revenge."

**I'm so sorry I had to leave it there! I was shooting for a cliffhanger and I succeeded! I know there's not a lot of Jace/Clary mush yet, but there will be in the next chapter. I promise! I've been thinking about this idea for about a month now and I thought it was high time I put it into action.**

**So, if you want more, you have to **_**review, review, review**_**! Let me know what you think and if you have any suggestions!!**


	2. Chapter 2

**Thanks to all of you who reviewed! I know a lot of you were asking about why Jace was taking it so hard on Clary and it'll semi be explained in this chapter. It'll be more so in the next chapter, but for now, I hope this'll hold you over!**

**Also, there are links to the pictures of Clary and Isabelle's clubbing clothes for this chapter on my profile!**

**The song I used for this chapter was:**

**_Love and Pain_ by New Found Glory. I think it goes well with the end of scene 1 with Clary, and then the end scene between Jace and Clary.**

**[Disclaimer: I don't own TMI. The brilliant Ms. Clare does.]**

**Chapter Two**

Jace sat forward in his seat almost immediately, his eyes trained on Maryse. He looked shocked and surprised, no doubt, but he was also curious as to who this person was. Clary, too, looked surprised but it was also accompanied by a sick feeling in the pit of her stomach, one of worry and fear.

"Who is it?" Alec asked his mother, tensing up slightly.

The atmosphere in the room had grown ridiculously heavy in the past several minutes since they had arrived and it felt like a weight was pressing down on Clary's chest, making it difficult for her to really breathe properly.

"Sebastian," Maryse said in a quiet voice, her gaze going from one teenager to the next as if letting them sink in the information separately. "Or Jonathan…whichever you decide to look at him as. Valentine's son, nonetheless….Clary's brother."

Clary felt her head whirl at this news and her eyes widened slightly, her breathing going a bit more shallow than normal. She couldn't swallow, she couldn't blink, she couldn't think. She just sat there and stared at her, wondering how on earth Jonathan could come back from the dead. Something wasn't right, she thought to herself. Something was wrong; very wrong.

Jace went completely still beside her, his hand gripping hers tightly but not so tight it would hurt; she felt comforted by the grip he had on her hand. As if he would protect her from any and everything. Just like he always had. She relied on him and she trusted him with her life and that wasn't about to stop any time soon.

"How?" Jace asked and Clary then noticed that most of the color had drained from his cheeks.

Maryse sighed and shook her head slowly. "That's the problem, Jace. I don't know. All we know is that he has been sighted but he fled before any Shadowhunters could get to him to restrain him. It was dark and on the outskirts of Idris," she said, her voice quiet and almost grave.

"Well what are we going to do? Did you call in reinforcements? Are they still out looking for that bastard?" Jace demanded.

"Jace," Maryse said sharply. "Language. But yes, they are still out searching for him. They have had no luck so far, though. I'm expecting to hear back any time now, though."

"But…if Jonathan is alive than what if Valentine is too?" Clary asked, speaking the words she feared most at that moment.

She saw Isabelle bit her lip, obviously thinking along the same lines as she was. If Jonathan was alive then there was no doubt that Valentine was too, or would be soon enough.

Maryse faltered for just a moment before she continued on, "I doubt that is a possibility. If he is then the Clave will know immediately and there will be more Shadowhunters and Downworlders after him than he ever could have thought possible." Her words were firm and full of confidence, something Clary knew that she herself lacked.

Jace's jaw tightened and he stood up abruptly to pace around the room, obviously needing something to do with himself. He looked angry, confused, and like he wanted nothing more than to hit something – a wall, a punching bag; something, anything.

Maryse watched him for a moment along with everyone else before she continued on, saying, "I wouldn't worry about it too much. A group of Shadowhunters are going to come here to make sure we all stay safe since they think that…Clary and Jace are the main targets here."

Jace looked at her and then at Clary. "You're not going out by yourself. Not without me, Alec, _and_ Isabelle with you."

Clary looked right back at him and crossed her arms over her chest. "You can't tell me what to do, Jace."

Maryse cleared her throat. "You are all free to go now," she said with a nod. Apparently she didn't want a lover's spat breaking out in the library. Clary didn't object and she got up, walking out of the room, annoyed at Jace suddenly. She walked upstairs to her room and she shut and locked the door before she got into the shower. She didn't care if Jace had been going to follow her to continue their "conversation".

She stood under the hot spray of water, closing her eyes, letting it loosen up her muscles. The bruises from the day before were already fading but the one on her arm from earlier looked fresh. She knew Jace didn't mean to hurt her. If he found out, she knew that he would be furious with himself, which is why she made sure to cover them up with long sleeves; it helped that winter was arriving fast in New York. Jace didn't know how own strength. He thought he did, but he didn't.

Clary sighed quietly to herself as she finally washed her hair and body, stepping out of the shower before she wrapped herself in a big, warm, fluffy towel.

She rubbed her hand over the surface of the mirror to get the steam off and she stared at her reflection. Her skin had beads of water clinging to her and her hair hung around her face, soaking wet. She briefly wondered why Jace wasn't so focused on being a boyfriend lately. His mind seemed elsewhere and he never just held her for the heck of it. She wondered if she was doing something wrong; she wondered if she wasn't pretty enough or not strong enough, or not a good enough Shadowhunter. Well, she would change all those things if she had to.

* * *

"Jace Lightwood, open this door!" Isabelle said, pounding her fist against the wood continuously as she stood there, free hand perched on her hip.

Jace rolled his eyes on the other side and gave a sigh, towel wrapped around his waist from his shower, drops of water running down his chest from his damp blond hair. He reached out and opened the door. "Yes, Isabelle?"

Isabelle looked at him and fixed her eyes on his face. He wondered how the hell she could see him standing there, half naked, and not be totally and completely affected by it. It blew his mind sometimes that a girl could do that. Not that he was interested in Isabelle anyway; she was like a sister and besides, he loved Clary – no one else. "I want to talk to you," Isabelle said to him. "You need to take it easy on Clary in training. She's just jumping into this – you, Alec, and I have been training since we could learn to walk pretty much. Clary hasn't. You should see the bruises you put all over her."

Jace's smirk disappeared. "What? Bruises?"

"By the Angel, Jace," she sighed exasperatedly. "Do you really not see it? Do you really not see how sore she is? How hard you're going on her?"

Jace swallowed hard and said, "I…I didn't know, Izzy. I swear I didn't. She never said anything about it."

"No, she didn't say anything about it because she didn't want you to think she was weak. She didn't want you to treat her special just because she's your girlfriend," Isabelle told him with a sigh, letting her hands drop down to her sides.

"I just want to make sure she's well trained so she can defend herself if I'm ever unable to," he said, looking at her. A sigh escaped his lips. "Damnit." He ran one strong hand through his blonde hair, looking frustrated. He was frustrated with himself; not Clary, never Clary.

"You need to talk to her," Isabelle said quietly.

"I know. I will – right now. But Izzy, you need to lay off a little, okay? I'm tired of being verbally abused by you," Jace said with a smirk, his old sarcastic nature coming back. "I need to get dressed – and don't complain, even though I know you just love looking at me half naked. I mean, come on, who wouldn't?" He closed the door leaving Isabelle rolling her eyes before she walked down the hallway to her room.

* * *

When Isabelle walked in her room, she blinked in surprise when she saw Clary, clad in just clean sweatpants and a tank top, sitting on her bed. "Oh, hello, Clary," she said, shutting the door behind her. "What brings you to this end of the hallway?"

Clary tried to smile but she was too nervous for that. "Izzy, I need your help. I really need your help."

Isabelle smiled. "I've been wondering when you would admit it to yourself. Let's go through my closet," she said, walking over to it and throwing the door open, looking through all her clothes, trying to find the perfect outfit. She tossed pieces of clothes at Clary, telling her to try them on. When Isabelle would shake her head with a grimace, Clary pulled the clothing off and waited until Isabelle found something else. Finally, Isabelle let out a triumphant, "Ah ha!" and tossed a gray and black top at Clary. It was a kind of long gray knit top that obviously came down to Isabelle's hips while it reached down to Clary's thighs, only inches below her butt. It had a black belt around the waist, a black neckline and black sleeve trims. It was very cute but Clary wondered if it would look alright on her.

"Put it on," Isabelle instructed as she pulled a pair of black thigh-high boots out of the bottom of her closet.

Clary bit her lip slightly before she pulled the fabric over her head and let it slide down into place. It fit to every curve of her body. Isabelle helped put the boots on her feet. She pulled Clary over to the mirror and grinned, "Girl, you look hot," she said.

Clary looked at her. "I look like I'm trying too hard."

Isabelle rolled her eyes. "Clary, just trust me." She took hold of Clary's shoulders. "I'm telling Jace that tonight we're all going to Pandemonium. You can't just not go out in an outfit like that."

Clary's eyes widened. "I have to go out in public like this?" she exclaimed.

"Oh, that wounds me," Isabelle said, but she wasn't being really serious at all. She walked over and grabbed a black tube mini dress, pulling it on. It looked perfect on her and went incredibly with her long black hair. She pulled on a pair of black leather platform sandal boots and applied lip gloss. "I'll go tell the boys. Put on some mascara and lip gloss and meet us downstairs," she instructed her before she slipped out, walking down the hall.

Clary examined herself in the mirror. She had to admit, she did look…pretty good. Pretty good, however, was an understatement but she just thought the freckles took away from the sexy look she was hoping for. She grimaced slightly and grabbed the mascara tube, applying it carefully to her lashes before she swiped some lip gloss over her lips, running her fingers through her hair to make it messy in a hopefully sexy sort of way. That was what she was praying for, anyway.

"Clary, c'mon!" Isabelle called from the top of the stairs several minutes later.

Clary took a deep breath before she finally walked out of Isabelle's room, walking down the hall. She didn't see the boys.

"They're waiting downstairs," Isabelle said, answering Clary's unspoken question.

"Are you sure I look all right?" Clary asked her, feeling self conscious as she tugged down the hem of the dress.

"Stop fidgeting, you look fine," Isabelle said, grabbing her arm. Her bruise was barely visible and she made a point not to acknowledge it. She tugged her downstairs with her and Clary's face flushed pink at Jace's expression.

His tawny eyes were wide, his jaw slack as he leaned against the doorway with his hands in his black jean pockets. He was wearing a white shirt with it which showed off his dark Marks under it in just the right lighting. It was buttoned only halfway, showing off the muscled planes of his toned chest.

"Wow," he said quietly as his eyes surveyed Clary.

"Told you," Isabelle said triumphantly, looking proud of herself. "Thank you, Isabelle."

Clary smiled, "Thanks, Izzy," she said, saying what the other girl wanted to hear.

Jace stepped forward and took Clary's hand and he pulled her against him. He pressed his mouth to hers in a sweet, gentle kiss, his hands coming up to cradle her face. Clary's fingers brushed against the fabric of his shirt at his chest, drinking in everything about him, his closeness, his scent, his strength. She loved him.

"Ahem," Alec said with a smirk behind them and Jace raised his hand in a rude gesture involving only one finger.

Jace finally broke the kiss and he looked down at her and her arm. He raised her forearm to his lips and pressed his lips over the light purple bruise. "I'm so sorry," he murmured quietly, brushing the fingers of his free hand over her cheek. "I didn't mean to hurt you."

Clary smiled a small smile, brushing her fingers through his blond curls. "It's fine," she promised."

Isabelle grinned. "Now let's go clubbing!"

**Well, there it is! I hope you liked it. Was it okay? Did it answer your questions? I want lots of reviews! The more reviews I get, the faster I write, so keep 'em coming!**


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